Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015116.1 Corchorus capsularis cultivar CVL-1 contig15137, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5112
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Found at i:1086 original size:28 final size:27
Alignment explanation
Indices: 1023--1128 Score: 149
Period size: 27 Copynumber: 3.9 Consensus size: 27
1013 ATTAGGGTCG
* *
1023 CCCAAGGGTATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
**
1050 CGTAGGGGCATTTTGGTCATTTTTGCA
1 CCCAGGGGCATTTTGGTCATTTTTGCA
1077 CCCAGGGGGCATTTTGGTCATTTTTGCA
1 CCCA-GGGGCATTTTGGTCATTTTTGCA
* *
1105 CTCAGGGGCATTTTAGTCATTTTT
1 CCCAGGGGCATTTTGGTCATTTTT
1129 AAGTTCACCT
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
27 44 0.63
28 26 0.37
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (27 bp):
CCCAGGGGCATTTTGGTCATTTTTGCA
Found at i:1300 original size:21 final size:21
Alignment explanation
Indices: 1258--1301 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1248 CATTATGGTG
*
1258 TTTTCAATTAGTAGTGTTGCA
1 TTTTCAATTAGTAATGTTGCA
*
1279 TTTTCATTTAGTAAT-TTGGCA
1 TTTTCAATTAGTAATGTT-GCA
1300 TT
1 TT
1302 GTTACACTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.52
Consensus pattern (21 bp):
TTTTCAATTAGTAATGTTGCA
Found at i:4065 original size:30 final size:29
Alignment explanation
Indices: 4029--4097 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
4019 GACACCTTGG
*
4029 AATAAAAATTGAAATTTCAAGTAATTTGAA
1 AATAAAAATT-AAATTTCAAGTAATTAGAA
* ** *
4059 AATAAAAGATTTAATTTTTAGTAATTAGTA
1 AATAAAA-ATTAAATTTCAAGTAATTAGAA
4089 AATAAAAAT
1 AATAAAAAT
4098 GTCATCTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 2 0.06
30 28 0.85
31 3 0.09
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (29 bp):
AATAAAAATTAAATTTCAAGTAATTAGAA
Found at i:4132 original size:49 final size:49
Alignment explanation
Indices: 4060--4416 Score: 410
Period size: 49 Copynumber: 7.4 Consensus size: 49
4050 TAATTTGAAA
* *
4060 ATAAAAGATTTAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTAT
1 ATAAAAGATTGAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTAG
* *
4109 ATAAAAGATTTAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTAA
1 ATAAAAGATTGAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTAG
* *
4158 ATAAAAGATTTAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTGG
1 ATAAAAGATTGAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTAG
* *
4207 GTAAAAGATTGAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTGG
1 ATAAAAGATTGAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTAG
* * *
4256 GTAAAAGATTGAATTTTTAGT-A--AG----TAAAAATGTCACCGTTGAG
1 ATAAAAGATTGAATTTTTAGTAATTAGTAAATAAAAATGTCATC-TTTAG
* * * *
4299 A-AAAAGATTGAATTTCTAAGTAATTAGTAAGTAAAAACGTCACCTTT-G
1 ATAAAAGATTGAATTT-TTAGTAATTAGTAAATAAAAATGTCATCTTTAG
* ** * * *
4347 AGCAAAAGATTGAATTTTTAAGTAATTAGTAAATAAGGACGTAACCTTT-G
1 A-TAAAAGATTGAATTTTT-AGTAATTAGTAAATAAAAATGTCATCTTTAG
4397 AATAAAAGATTGAATTTTTA
1 -ATAAAAGATTGAATTTTTA
4417 AAAAAGTAAT
Statistics
Matches: 277, Mismatches: 18, Indels: 26
0.86 0.06 0.08
Matches are distributed among these distances:
42 26 0.09
43 7 0.03
44 1 0.00
46 4 0.01
48 3 0.01
49 167 0.60
50 68 0.25
51 1 0.00
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (49 bp):
ATAAAAGATTGAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTAG
Found at i:4181 original size:98 final size:98
Alignment explanation
Indices: 4058--4456 Score: 413
Period size: 98 Copynumber: 4.1 Consensus size: 98
4048 AGTAATTTGA
* * *
4058 AAATAAAAGATTTAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTATATAAAAGATTTAAT
1 AAATAAAAGATTGAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTAGATAAAAGATTGAAT
4123 TTTTAGTAATTAGTAAATAAAAATGTCATCTTT
66 TTTTAGTAATTAGTAAATAAAAATGTCATCTTT
* * *
4156 AAATAAAAGATTTAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTGGGTAAAAGATTGAAT
1 AAATAAAAGATTGAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTAGATAAAAGATTGAAT
4221 TTTTAGTAATTAGTAAATAAAAATGTCATCTTT
66 TTTTAGTAATTAGTAAATAAAAATGTCATCTTT
*** * *
4254 GGGTAAAAGATTGAATTTTTAGT-A--AG----TAAAAATGTCACCGTTGAGA-AAAAGATTGAA
1 AAATAAAAGATTGAATTTTTAGTAATTAGTAAATAAAAATGTCATC-TTTAGATAAAAGATTGAA
* * * *
4311 TTTCTAAGTAATTAGTAAGTAAAAACGTCACCTTT
65 TTT-TTAGTAATTAGTAAATAAAAATGTCATCTTT
* ** ** * * *
4346 GAGCAAAAGATTGAATTTTTAAGTAATTAGTAAATAAGGACGTAACCTTT-GAATAAAAGATTGA
1 AAATAAAAGATTGAATTTTT-AGTAATTAGTAAATAAAAATGTCATCTTTAG-ATAAAAGATTGA
* *
4410 ATTTTTAAAAAAGTAATTCGTGAAT-AAAATGTCATCTTT
64 ATTTTT-----AGTAATTAGTAAATAAAAATGTCATCTTT
*
4449 GAATAAAA
1 AAATAAAA
4457 TTTTGAACTT
Statistics
Matches: 253, Mismatches: 31, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
91 26 0.10
92 48 0.19
93 3 0.01
94 1 0.00
95 2 0.01
96 2 0.01
97 1 0.00
98 114 0.45
99 4 0.02
100 23 0.09
103 18 0.07
104 11 0.04
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (98 bp):
AAATAAAAGATTGAATTTTTAGTAATTAGTAAATAAAAATGTCATCTTTAGATAAAAGATTGAAT
TTTTAGTAATTAGTAAATAAAAATGTCATCTTT
Found at i:4289 original size:42 final size:42
Alignment explanation
Indices: 4230--4313 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
4220 TTTTTAGTAA
* * * *
4230 TTAGTAAATAAAAATGTCATCTTTGGGTAAAAGATTGAATTT
1 TTAGTAAATAAAAATGTCACCGTTGAGAAAAAGATTGAATTT
*
4272 TTAGTAAGTAAAAATGTCACCGTTGAGAAAAAGATTGAATTT
1 TTAGTAAATAAAAATGTCACCGTTGAGAAAAAGATTGAATTT
4314 CTAAGTAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.35
Consensus pattern (42 bp):
TTAGTAAATAAAAATGTCACCGTTGAGAAAAAGATTGAATTT
Found at i:4331 original size:50 final size:50
Alignment explanation
Indices: 4272--4413 Score: 196
Period size: 50 Copynumber: 2.8 Consensus size: 50
4262 GATTGAATTT
* *
4272 TTAGTAAGTAAAAATGTCACCGTTGAGAAAAAGATTGAATTTCTAAGTAA
1 TTAGTAAGTAAAAACGTCACCTTTGAGAAAAAGATTGAATTTCTAAGTAA
* *
4322 TTAGTAAGTAAAAACGTCACCTTTGAGCAAAAGATTGAATTTTTAAGTAA
1 TTAGTAAGTAAAAACGTCACCTTTGAGAAAAAGATTGAATTTCTAAGTAA
* ** *
4372 TTAGTAAATAAGGACGTAACCTTTGA-ATAAAAGATTGAATTT
1 TTAGTAAGTAAAAACGTCACCTTTGAGA-AAAAGATTGAATTT
4414 TTAAAAAAGT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
50 82 1.00
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (50 bp):
TTAGTAAGTAAAAACGTCACCTTTGAGAAAAAGATTGAATTTCTAAGTAA
Found at i:4358 original size:92 final size:91
Alignment explanation
Indices: 4181--4371 Score: 265
Period size: 92 Copynumber: 2.1 Consensus size: 91
4171 TTTTTAGTAA
* * * * * *
4181 TTAGTAAATAAAAATGTCATCTTTGGGTAAAAGATTGAATTTTTAGTAATTAGTAAATAAAAATG
1 TTAGTAAATAAAAATGTCACCGTTGAGAAAAAGATTGAATTTTAAGTAATTAGTAAATAAAAACG
* * *
4246 TCATCTTTGGGTAAAAGATTGAATTT
66 TCACCTTTGAGCAAAAGATTGAATTT
* *
4272 TTAGTAAGTAAAAATGTCACCGTTGAGAAAAAGATTGAATTTCTAAGTAATTAGTAAGTAAAAAC
1 TTAGTAAATAAAAATGTCACCGTTGAGAAAAAGATTGAATTT-TAAGTAATTAGTAAATAAAAAC
4337 GTCACCTTTGAGCAAAAGATTGAATTT
65 GTCACCTTTGAGCAAAAGATTGAATTT
4364 TTAAGTAA
1 TT-AGTAA
4372 TTAGTAAATA
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
91 37 0.43
92 45 0.52
93 5 0.06
ACGTcount: A:0.42, C:0.07, G:0.17, T:0.35
Consensus pattern (91 bp):
TTAGTAAATAAAAATGTCACCGTTGAGAAAAAGATTGAATTTTAAGTAATTAGTAAATAAAAACG
TCACCTTTGAGCAAAAGATTGAATTT
Done.